Bioinformatics Multiple Choice Questions on “Protein Structural Visualization”.
1. The main feature of computer visualization programs is interactivity, which allows users to visually manipulate the structural images through a graphical user interface. Answer: A 2. A Protein Data Bank (PDB. data file for a protein structure contains only x, and z coordinates of atoms. Answer: B 3. A wire-frame diagram is a line drawing representing bonds between atoms. Answer: A 4. Balls and sticks are solid spheres and rods, representing atoms and bonds, respectively. Answer: A 5. Ribbon diagrams use cylinders or spiral ribbons to represent α-helices and broad, flat arrows to represent β-strands. Answer: A 6. Different representation styles can be used in combination to highlight a certain feature of a structure while deemphasizing the structures surrounding it. Answer: A 7. Which of the following is wrong about Swiss-PDB Viewer? Answer: B 8. Which of the following is an incorrect statement? Answer: B 9. Which of the following is an incorrect statement? Answer: c 10. Ribbons another UNIX program similar to Molscript, generates ribbon diagrams depicting protein secondary structures. Answer: A
A. True
B. False
Explanation: At the touch of a mouse button, a user can move, rotate, and zoom an atomic model on a computer screen in real time, or examine any portion of the structure in great detail, as well as draw it in various forms in different colors. Further manipulations can include changing the conformation of a structure by protein modeling or matching a ligand to an enzyme active site through docking exercises.
A. True
B. False
Explanation: Because a Protein Data Bank (PDB. data file for a protein structure contains only x, y, and z coordinates of atoms, the most basic requirement for a visualization program is to build connectivity between atoms to make a view of a molecule. The visualization program should also be able to produce molecular structures in different styles, which include wire frames, balls and sticks, space-filling spheres, and ribbons.
A. True
B. False
Explanation: The wire frame is the simplest form of model representation. It is useful for localizing positions of specific residues in a protein structure, or for displaying a skeletal form of a structure when Cα atoms of each residue are connected.
A. True
B. False
Explanation: These diagrams can also be used to represent the backbone of a structure. In a space-filling representation, each atom is described using large solid spheres with radii corresponding to the van der Waals radii of the atoms.
A. True
B. False
Explanation: This type of representation is very attractive in that it allows easy identification of secondary structure elements and gives a clear view of the overall topology of the structure. The resulting images are also visually appealing.
A. True
B. False
Explanation: For example, a cofactor of an enzyme can be shown as space-filling spheres while the rest of the protein structure is shown as wire frames or ribbons. Some widely used and freely available software programs are there for molecular graphics.
A. It is a structure viewer for multiple platforms
B. It is a structure viewer for single platforms
C. It is essentially a Swiss-Army knife for structure visualization and modeling
D. It is capable of structure visualization, analysis, and homology modeling
Explanation: It is essentially a Swiss-Army knife for structure visualization and modeling because it incorporates so many functions in a small shareware program. It allows display of multiple structures at the same time in different styles, by charge distribution, or by surface accessibility. It can measure distances, angles, and even mutate residues. In addition, it can calculate molecular surface, electrostatic potential, Ramachandran plot, and so on. The homology modeling part includes energy minimization and loop modeling.
A. WebMol is a web-based program built based on a modified RasMol code and thus shares many similarities with RasMol
B. WebMol is a web-based program that is totally different from RasMol
C. Chime is a plug-in for web browsers
D. Chime is not a standalone program and has to be invoked in a web browser
Explanation: Chime is also derived from RasMol and allows interactive display of graphics of protein structures inside a web browser. RasMol runs directly on a browser of any type as an applet and is able to display simple line drawing models of protein structures. It also has a feature of interactively displaying Ramachandran plots for structure model evaluation.
A. Molscript is a UNIX program capable of generating wire-frame
B. Molscript is capable of generating space-filling
C. Molscript is not capable of generating ball-and-stick styles
D. In particular, secondary structure elements can be drawn with solid spirals and arrows representing α-helices and β-strands, respectively
Explanation: Visually appealing images can be generated that are of publication quality. The drawback is that the program is command-line–based and not very user friendly. A modified UNIX program called Bobscript is available with enhanced features.
A. True
B. False
Explanation: Aesthetically appealing images can be produced that are of publication quality. However, the program, which is also command-line-based, is extremely difficult to use.